n3d fixed. apicoBasalNeighbours replacing lateralSides

lib/featuresExtraction/calculate3DMorphologicalFeatures.m

@@ -21,8 +21,8 @@
 
         %% Calculate mean and std of 3D features
         cells3dFeatures((cells3dFeatures.ID_Cell == "Lumen" | cells3dFeatures.ID_Cell == "Tissue and Lumen"),:)=[];
-        meanCellsFeatures = varfun(@(x) mean(x),cells3dFeatures(:, 2:end-2));
-        stdCellsFeatures = varfun(@(x) std(x),cells3dFeatures(:, 2:end-2));
+        meanCellsFeatures = varfun(@(x) mean(x),cells3dFeatures(:, [(2:end-3),end]));
+        stdCellsFeatures = varfun(@(x) std(x),cells3dFeatures(:, [(2:end-3),end]));
 
         % Voxels/Pixels to Micrometers
         [totalMeanCellsFeatures,totalStdCellsFeatures, tissue3dFeatures, allLumens,allHollowTissue3dFeatures] = convertPixelsToMicrons(meanCellsFeatures,stdCellsFeatures, tissue3dFeatures, lumen3dFeatures,hollowTissue3dFeatures,pixelScale);
@@ -32,7 +32,6 @@
 
         save(fullfile(path2save, 'global_3dFeatures.mat'), 'allGeneralInfo', 'totalMeanCellsFeatures','totalStdCellsFeatures', 'allLumens', 'allTissues', 'allNetworkFeatures', 'allHollowTissue3dFeatures');
     else
-
         load(fullfile(path2save, 'global_3dFeatures.mat'), 'allGeneralInfo', 'totalMeanCellsFeatures','totalStdCellsFeatures', 'allLumens', 'allTissues', 'allNetworkFeatures', 'allHollowTissue3dFeatures');
     end
 

lib/featuresExtraction/calculate_CellularFeatures.m

@@ -13,7 +13,7 @@
 
     %%  Calculate number of neighbours of each cell
     number_neighbours = table(cellfun(@length,(apical3dInfo)),cellfun(@length,(basal3dInfo)),cellfun(@length,(lateral3dInfo)));
-    
+
     apicobasal_neighbours=cellfun(@(x,y)(unique(vertcat(x,y))), apical3dInfo, basal3dInfo, 'UniformOutput',false);
     apicobasal_neighboursRecount= cellfun(@length ,apicobasal_neighbours);
 
@@ -31,9 +31,9 @@
     volume_cells=table2array(regionprops3(labelledImage,'Volume'));
 
     %%  Determine if a cell is a scutoid or not
-    scutoids_cells=cellfun(@(x,y) double(~isequal(x,y)), neighbours_data.Apical,neighbours_data.Basal);
-    apicoBasalTransitions = cellfun(@(x, y) length(unique(vertcat(setdiff(x, y), setdiff(y, x)))), neighbours_data.Apical,neighbours_data.Basal);
-    
+    apicoBasalTransitions = cellfun(@(x, y) length(unique(vertcat(setdiff(y,x), setdiff(x,y)))), neighbours_data.Apical,neighbours_data.Basal);
+    scutoids_cells = double(apicoBasalTransitions>0);
+
     %% Calculate cell height
     cell_heights = calculateCellHeight(apicalLayer, basalLayer);
 

lib/featuresExtraction/obtain3DFeatures.m

@@ -6,8 +6,6 @@
         dilatedVx = 4;
         [lateral3dInfo_total,totalLateralCellsArea,absoluteLateralContacts] = getLateralContacts(lateralLayer,dilatedVx,contactThreshold);
 
-        %lateral3dInfo = lateral3dInfo.neighbourhood';
-
         %% Cellular features 
         [apical3dInfo] = calculateNeighbours3D(apicalLayer, dilatedVx, apicalLayer == 0);
         apical3dInfo = cellfun(@(x,y) intersect(x,y),lateral3dInfo_total,apical3dInfo.neighbourhood','UniformOutput',false);
@@ -26,11 +24,6 @@
             lateral3dInfo = lateral3dInfo_total;
             clearvars lateral3dInfo_total lateralLayerAux
         end
-
-        %delete non real neighbours assuming lateral contact threshold
-        apical3dInfo = cellfun(@(x,y) x(ismember(x,y)), apical3dInfo,lateral3dInfo,'UniformOutput',false);
-        basal3dInfo = cellfun(@(x,y) x(ismember(x,y)), basal3dInfo,lateral3dInfo,'UniformOutput',false);
-
 
         %check for non considered valid cells, and delete cells "0" volume
         missingCells = find(totalLateralCellsArea==0);
@@ -80,13 +73,13 @@
         refactorLateralAreas = cellularFeaturesValidCells.Lateral_area./lateralAreas;
 
         cellAreaNeighsInfo = table(cellularFeaturesValidCells.Apical_sides, cellularFeaturesValidCells.Apical_area./refactorApicalAreas,cellularFeaturesValidCells.Basal_sides, cellularFeaturesValidCells.Basal_area./refactorBasalAreas,cellularFeaturesValidCells.Cell_height,cellularFeaturesValidCells.Lateral_sides, cellularFeaturesValidCells.Lateral_area./refactorLateralAreas,cellularFeaturesValidCells.Average_cell_wall_area./refactorLateralAreas,cellularFeaturesValidCells.Std_cell_wall_area./refactorLateralAreas,'VariableNames',{'apical_NumNeighs','apical_Area','basal_NumNeighs','basal_Area','cell_height','lateral_NumNeighs','lateral_Area','average_cell_wall_Area','std_cell_wall_Area'});
-        cells3dFeatures = horzcat(cells3dFeatures, cellAreaNeighsInfo,table(cellularFeaturesValidCells.Scutoids, cellularFeaturesValidCells.apicoBasalTransitions,'VariableNames',{'scutoids','apicoBasalTransitions'}));
+        cells3dFeatures = horzcat(cells3dFeatures, cellAreaNeighsInfo,table(cellularFeaturesValidCells.Scutoids, cellularFeaturesValidCells.apicoBasalTransitions,cellularFeaturesValidCells.Apicobasal_neighbours,'VariableNames',{'scutoids','apicoBasalTransitions','n3d_apicoBasalNeighbours'}));
 
         %% Save variables
         save(fullfile(path2save, 'morphological3dFeatures.mat'), 'cells3dFeatures', 'tissue3dFeatures', 'lumen3dFeatures', 'polygon_distribution_apical', 'polygon_distribution_basal','polygon_distribution_lateral', 'cellularFeaturesValidCells', 'numValidCells','numTotalCells', 'surfaceRatio3D', 'polygon_distribution_lateral','apicoBasalNeighs', 'hollowTissue3dFeatures','apical3dInfo','basal3dInfo','lateral3dInfo');
 
     else
-        load(fullfile(path2save, 'morphological3dFeatures.mat'), 'cells3dFeatures', 'tissue3dFeatures', 'lumen3dFeatures', 'polygon_distribution_apical', 'polygon_distribution_basal','polygon_distribution_lateral', 'cellularFeaturesValidCells', 'numValidCells','numTotalCells', 'surfaceRatio3D', 'polygon_distribution_lateral','apicoBasalNeighs', 'hollowTissue3dFeatures','apical3dInfo','basal3dInfo','lateral3dInfo');
+        load(fullfile(path2save, 'morphological3dFeatures.mat'), 'cells3dFeatures', 'tissue3dFeatures', 'lumen3dFeatures', 'polygon_distribution_apical', 'polygon_distribution_basal','polygon_distribution_lateral', 'cellularFeaturesValidCells', 'numValidCells','numTotalCells', 'surfaceRatio3D', 'polygon_distribution_lateral','apicoBasalNeighs', 'hollowTissue3dFeatures','apical3dInfo','basal3dInfo','lateral3dInfo');        
     end
 end
 

lib/featuresExtraction/summarizeAllTissuesProperties.m

@@ -1,41 +1,34 @@
 function summarizeAllTissuesProperties(allGeneralInfo,allTissues,allLumens,allHollowTissue3dFeatures,allNetworkFeatures,totalMeanCellsFeatures,totalStdCellsFeatures,path2save)
 
-
     allGeneralInfo = vertcat(allGeneralInfo{:});
     allTissues = vertcat(allTissues{:});
     allLumens = vertcat(allLumens{:});
     allHollowTissue3dFeatures = vertcat(allHollowTissue3dFeatures{:});
     allNetworkFeatures= vertcat(allNetworkFeatures{:});
     totalMeanCellsFeatures = vertcat(totalMeanCellsFeatures{:});
     totalStdCellsFeatures = vertcat(totalStdCellsFeatures{:});
-
 
     allTissues.Properties.VariableNames = cellfun(@(x) strcat('Tissue_', x), allTissues.Properties.VariableNames, 'UniformOutput', false);
     allHollowTissue3dFeatures.Properties.VariableNames = cellfun(@(x) strcat('HollowTissue_', x), allHollowTissue3dFeatures.Properties.VariableNames, 'UniformOutput', false);
     allLumens.Properties.VariableNames = cellfun(@(x) strcat('Lumen_', x), allLumens.Properties.VariableNames, 'UniformOutput', false);
     totalMeanCellsFeatures.Properties.VariableNames = cellfun(@(x) strcat('AverageCell_', x(5:end)), totalMeanCellsFeatures.Properties.VariableNames, 'UniformOutput', false);
     totalStdCellsFeatures.Properties.VariableNames = cellfun(@(x) strcat('STDCell_', x(5:end)), totalStdCellsFeatures.Properties.VariableNames, 'UniformOutput', false);
-
 
     PercentageLumenSpace = table(allLumens.Lumen_Volume./allTissues.Tissue_Volume,'VariableNames',{'PercentageLumenSpace'});
     FeaturesPerCell=table(allTissues.Tissue_Volume./allGeneralInfo.NCells_total, allHollowTissue3dFeatures.HollowTissue_Volume./allGeneralInfo.NCells_total, allLumens.Lumen_Volume./allGeneralInfo.NCells_total,'VariableNames',{'TissueVolume_perCell','HollowTissueVolume_perCell','LumenVolume_perCell'});
 
-
     %%Global parameters
     globalFeatures = [allGeneralInfo(:,[1,4,3]),allTissues(:,[4,8]),allHollowTissue3dFeatures(:,2),PercentageLumenSpace(:,1),allGeneralInfo(:,[2,5,6]),allTissues(:,[6,2,5,7,9,11]),FeaturesPerCell,allLumens(:,[6,2,5,7,9,4,8,11]),allHollowTissue3dFeatures(:,[6,7,9,4,8])];
     writetable(globalFeatures, [path2save,'global_3dFeatures_' date '.xls'],'Sheet', 'globalFeatures','Range','B2');
     %%Polygon distribtutions
     polDistributions = [allGeneralInfo(:,1),allTissues(:,12:35)];
     writetable(polDistributions, [path2save,'global_3dFeatures_' date '.xls'],'Sheet', 'polygonDistributions','Range','B2');
     %%Celullar parameters
-    cellularParameter_mean = [allGeneralInfo(:,1),totalMeanCellsFeatures(:,[12,14,15,17,18,19,1,11,13,16,4,5,6,8,3,7,10]),allNetworkFeatures(:,[1,2])];
+    cellularParameter_mean = [allGeneralInfo(:,1),totalMeanCellsFeatures(:,[12,14,15,17,18,19,1,11,13,16,end,4,5,6,8,3,7,10]),allNetworkFeatures(:,[1,2])];
     writetable(cellularParameter_mean, [path2save,'global_3dFeatures_' date '.xls'],'Sheet', 'meanCellParameters','Range','B2');
 
     %%Std parameters
-    cellularParameter_std = [allGeneralInfo(:,1),totalStdCellsFeatures(:,[12,14,15,17,18,19,1,11,13,16,4,5,6,8,3,7,10]),allNetworkFeatures(:,[4,5])];
-    writetable(cellularParameter_std, [path2save,'global_3dFeatures_' date '.xls'],'Sheet', 'stdCellParameters','Range','B2');
-
-
-
+    cellularParameter_std = [allGeneralInfo(:,1),totalStdCellsFeatures(:,[12,14,15,17,18,19,1,11,13,16,end,4,5,6,8,3,7,10]),allNetworkFeatures(:,[4,5])];
+    writetable(cellularParameter_std, [path2save,'global_3dFeatures_' date '.xls'],'Sheet', 'stdCellParameters','Range','B2');   
 end